Abstract:
BACKGROUND : Microsatellites or simple sequence repeats (SSRs) are DNA sequences consisting of 1–6 bp tandem
repeat motifs present in the genome. SSRs are considered to be one of the most powerful tools in genetic studies.
We carried out a comparative study of perfect SSR loci belonging to class I (≥20) and class II (≥12 and <20 bp)
types located in coding regions of high confidence genes in Picea abies and Pinus taeda. SSRLocator was used to
retrieve SSRs from the full length CDS of predicted genes in both species.
RESULTS : Trimers were the most abundant motifs in class I followed by hexamers in Picea abies, while trimers and
hexamers were equally abundant in Pinus taeda class I SSRs. Hexamers were most frequent within class II SSRs
followed by trimers, in both species. Although the frequency of genes containing SSRs was slightly higher in Pinus
taeda, SSR counts per Mbp for class I was similar in both species (P-value = 0.22); while for class II SSRs, it was
significantly higher in Picea abies (P-value = 0.00009). AT-rich motifs were higher in abundance than the GC-rich
motifs, within class II SSRs in both the species (P-values = 10−9 and 0). With reference to class I SSRs, AT-rich and
GC-rich motifs were detected with equal frequency in Pinus taeda (P-value = 0.24); while in Picea abies, GC-rich
motifs were detected with higher frequency than the AT-rich motifs (P-value = 0.0005).
CONCLUSIONS : Our study gives a comparative overview of the genome SSRs composition based on high confidence
genes in the two recently sequenced and economically important conifers and, also provides information on functional
molecular markers that can be applied in genetic studies in Pinus and Picea species.
